2 !-----------------------------------------------------------------------------
4 !-----------------------------------------------------------------------------
5 ! Max. number of energy intervals
6 integer,parameter :: max_ene=49 !10
7 !-----------------------------------------------------------------------------
8 ! Maximum number of terms in SC bond-stretching potential
9 integer,parameter :: maxbondterm=3
10 !-----------------------------------------------------------------------------
11 ! Max. number of derivatives of virtual-bond and side-chain vectors in theta
14 !-----------------------------------------------------------------------------
15 ! Max. number of contacts per residue
17 integer,parameter :: maxcontsshi=50
18 !-----------------------------------------------------------------------------
19 ! Max. number of SC contacts
21 !-----------------------------------------------------------------------------
24 integer :: ncont,ncont_ref
25 integer,dimension(:,:),allocatable :: icont,icont_ref !(2,maxcont)
27 ! integer,dimension(:),allocatable :: nsccont_frag_ref !(mmaxfrag) !wham
28 ! integer,dimension(:,:,:),allocatable :: isccont_frag_ref !(2,maxcont,mmaxfrag) !wham
30 ! 12/13/2008 (again Poland-Jaruzel war anniversary)
31 ! RE: Parallelization of 4th and higher order loc-el correlations
32 ! common /contdistrib/
33 integer,dimension(:),allocatable :: iat_sent !(maxres)
34 ! iat_sent - zainicjowane w initialize_p.F;
35 integer,dimension(:,:,:),allocatable :: iint_sent,iint_sent_local !(4,maxres,maxres)
36 integer,dimension(:,:),allocatable :: iturn3_sent,iturn4_sent,&
37 iturn3_sent_local,iturn4_sent_local !(4,maxres),
38 integer,dimension(:),allocatable :: itask_cont_from,itask_cont_to !(0:max_fg_procs-1),
39 integer :: nat_sent,ntask_cont_from,ntask_cont_to
40 !-----------------------------------------------------------------------------
43 real(kind=8),dimension(:,:),allocatable :: dcdv,dxdv !(6,maxdim)
44 real(kind=8),dimension(:,:),allocatable :: dxds !(6,maxres)
45 real(kind=8),dimension(:,:,:),allocatable :: gradx,gradc !(3,maxres,2)
46 real(kind=8),dimension(:,:),allocatable :: gvdwx !(3,maxres)
47 real(kind=8),dimension(:,:),allocatable :: gloc,gloc_x !(maxvar,2) ,gloc_x !!! nie używane
48 real(kind=8),dimension(:,:,:),allocatable :: dtheta !(3,2,maxres)
49 real(kind=8),dimension(:,:,:),allocatable :: dphi,dalpha,domega !(3,3,maxres)
52 ! common /derivat/ wham
55 integer :: igrad_start,igrad_end
56 integer,dimension(:),allocatable :: jgrad_start,jgrad_end !(maxres)
57 !-----------------------------------------------------------------------------
58 ! The following COMMON block selects the type of the force field used in
59 ! calculations and defines weights of various energy terms.
61 !-----------------------------------------------------------------------------
65 integer :: rescale_mode
66 real(kind=8) :: wsc,wscp,welec,wbond,wstrain,wtor,wtor_d,wang,&
67 wscloc,wcorr,wcorr4,wcorr5,wcorr6,wsccor,wel_loc,wturn3,wturn4,&
68 wturn6,wvdwpp,wliptran,wshield,lipscale,wtube, &
69 wbond_nucl,wang_nucl,wcorr_nucl,wcorr3_nucl,welpp,wtor_nucl,&
70 wtor_d_nucl,welsb,wsbloc,wvdwsb,welpsb,wvdwpp_nucl,wvdwpsb,wcatprot,&
71 wcatcat,wscbase,wpepbase,wscpho,wpeppho
73 real(kind=8) :: scalscp
75 real(kind=8),dimension(:),allocatable :: weights !(n_ene)
76 real(kind=8) :: temp0,scal14,cutoff_corr,delt_corr,r0_corr
77 integer :: ipot,ipot_nucl
79 character(len=3),dimension(5) :: potname = &
80 (/'LJ ','LJK','BP ','GB ','GBV'/)
81 !-----------------------------------------------------------------------------
82 ! wlong,welec,wtor,wang,wscloc are the weight of the energy terms
83 ! corresponding to side-chain, electrostatic, torsional, valence-angle,
84 ! and local side-chain terms.
86 ! IPOT determines which SC...SC interaction potential will be used:
87 ! 1 - LJ: 2n-n Lennard-Jones
88 ! 2 - LJK: 2n-n Kihara type (shifted Lennard-Jones)
89 ! 3 - BP; Berne-Pechukas (angular dependence)
90 ! 4 - GB; Gay-Berne (angular dependence)
91 ! 5 - GBV; Gay-Berne-Vorobjev; angularly-dependent Kihara potential
92 !-----------------------------------------------------------------------------
95 real(kind=8),dimension(:,:),allocatable :: aa_aq,bb_aq,augm,aa_lip,bb_lip !(ntyp,ntyp)
96 real(kind=8),dimension(:),allocatable :: sc_aa_tube_par,sc_bb_tube_par,&
97 acavtub,bcavtub,ccavtub,dcavtub,tubetranene
98 real(kind=8),dimension(:,:),allocatable :: aa_nucl,bb_nucl
99 real(kind=8) :: acavtubpep,bcavtubpep,ccavtubpep,dcavtubpep, &
100 tubetranenepep,pep_aa_tube,pep_bb_tube,tubeR0
101 real(kind=8),dimension(3) :: tubecenter
102 real(kind=8),dimension(:,:),allocatable :: aad,bad !(ntyp,2)
103 real(kind=8),dimension(2,2) :: app,bpp,ael6,ael3
104 real(kind=8),dimension(:),allocatable :: aad_nucl,bad_nucl !(ntyp,2)
105 real(kind=8),dimension(2,2) :: app_nucl,bpp_nucl
106 real(kind=8),dimension(:,:),allocatable :: ael6_nucl,&
107 ael3_nucl,ael32_nucl,ael63_nucl
108 integer :: expon,expon2, nnt,nct,itypro
109 integer,dimension(5) :: nnt_molec,nct_molec
110 integer,dimension(:,:),allocatable :: istart,iend !(maxres,maxint_gr)
111 integer,dimension(:),allocatable :: nint_gr,itel,&
112 ielstart,ielend,ielstart_vdw,ielend_vdw,nscp_gr !(maxres)
113 integer,dimension(:,:),allocatable :: istart_nucl,iend_nucl !(maxres,maxint_gr)
114 integer,dimension(:),allocatable :: nint_gr_nucl,itel_nucl,&
115 ielstart_nucl,ielend_nucl,ielstart_vdw_nucl,ielend_vdw_nucl,nscp_gr_nucl !(maxres)
116 integer,dimension(:,:),allocatable :: iscpstart_nucl,iscpend_nucl !(maxres,maxint_gr)
118 integer,dimension(:),allocatable :: istype,molnum
119 integer,dimension(:,:),allocatable :: itype ! now itype has more molecule types
120 integer,dimension(:,:),allocatable :: iscpstart,iscpend !(maxres,maxint_gr)
121 integer :: iatsc_s,iatsc_e,iatel_s,iatel_e,iatel_s_vdw,&
122 iatel_e_vdw,iatscp_s,iatscp_e,ispp,iscp
123 integer :: iatsc_s_nucl,iatsc_e_nucl,iatel_s_nucl,iatel_e_nucl,&
124 iatel_s_vdw_nucl,iatel_e_vdw_nucl,iatscp_s_nucl,iatscp_e_nucl,&
127 ! 12/1/95 Array EPS included in the COMMON block.
129 real(kind=8),dimension(:,:),allocatable :: sigma !(0:ntyp1,0:ntyp1)
130 real(kind=8),dimension(:,:),allocatable :: eps,epslip,sigmaii,&
131 rs0,chi,r0,r0e !(ntyp,ntyp) r0e !!! nie używane
132 real(kind=8),dimension(:),allocatable :: chip,alp,sigma0,&
134 real(kind=8),dimension(2,2) :: rpp,epp,elpp6,elpp3
135 real(kind=8),dimension(:,:),allocatable :: sigma_nucl !(0:ntyp1,0:ntyp1)
136 real(kind=8),dimension(:,:),allocatable :: eps_nucl,sigmaii_nucl,&
137 chi_nucl,r0_nucl, chip_nucl !(ntyp,ntyp) r0e !!! nie używane
138 real(kind=8),dimension(:),allocatable :: alp_nucl,sigma0_nucl,&
139 sigii_nucl,rr0_nucl !(ntyp)
140 real(kind=8),dimension(2,2) :: rpp_nucl,epp_nucl
141 real(kind=8),dimension(:,:),allocatable ::elpp6_nucl,&
142 elpp3_nucl,elpp32_nucl,elpp63_nucl
143 real(kind=8):: r0pp,epspp,AEES,BEES
145 real(kind=8),dimension(:,:),allocatable :: r0d,eps_scp,rscp !(ntyp,2) r0d !!! nie używane
146 real(kind=8),dimension(:),allocatable :: eps_scp_nucl,rscp_nucl!(ntyp,2) r0d !!! nie używane
148 ! 12/5/03 modified 09/18/03 Bond stretching parameters.
150 real(kind=8) :: vbldp0,akp,distchainmax,vbldpDUM
151 real(kind=8),dimension(:,:),allocatable :: vbldsc0,aksc,abond0 !(maxbondterm,ntyp)
152 real(kind=8) :: vbldp0_nucl,akp_nucl
153 real(kind=8),dimension(:,:),allocatable :: vbldsc0_nucl,&
154 aksc_nucl,abond0_nucl !(maxbondterm,ntyp)
156 integer,dimension(:),allocatable :: nbondterm !(ntyp)
157 integer,dimension(:),allocatable :: nbondterm_nucl !(ntyp)
159 !-----------------------------------------------------------------------------
161 ! Parameters of ab initio-derived potential of virtual-bond-angle bending
162 ! common /theta_abinitio/
163 integer :: nthetyp,ntheterm,ntheterm2,ntheterm3,nsingle,&
165 integer,dimension(:),allocatable :: ithetyp !(-ntyp1:ntyp1)
166 integer,dimension(:,:),allocatable :: nstate !(-ntyp1:ntyp1)
167 real(kind=8),dimension(:,:,:,:),allocatable :: aa0thet
168 !(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
169 real(kind=8),dimension(:,:,:,:,:),allocatable :: aathet
170 real(kind=8),dimension(:,:,:,:,:,:),allocatable :: bbthet,&
172 !(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
173 real(kind=8),dimension(:,:,:,:,:,:,:),allocatable :: ffthet,ggthet
175 !-----------nucleic acid parameters--------------------------
176 integer :: nthetyp_nucl,ntheterm_nucl,ntheterm2_nucl,&
177 ntheterm3_nucl,nsingle_nucl,&
178 ndouble_nucl,nntheterm_nucl
179 integer,dimension(:),allocatable :: ithetyp_nucl !(-ntyp1:ntyp1)
180 real(kind=8),dimension(:,:,:),allocatable :: aa0thet_nucl
181 !(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
182 real(kind=8),dimension(:,:,:,:),allocatable :: aathet_nucl
183 real(kind=8),dimension(:,:,:,:,:),allocatable :: bbthet_nucl,&
184 ccthet_nucl,ddthet_nucl,eethet_nucl
185 !(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
186 real(kind=8),dimension(:,:,:,:,:,:),allocatable :: ffthet_nucl,ggthet_nucl
188 !(maxdouble,maxdouble,maxtheterm3,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
189 ! Parameters of the virtual-bond-angle probability distribution
191 real(kind=8),dimension(:),allocatable :: a0thet,theta0,&
192 sig0,sigc0 !(-ntyp:ntyp)
193 real(kind=8),dimension(:,:,:,:),allocatable :: athet,bthet !(2,-ntyp:ntyp,-1:1,-1:1)
194 real(kind=8),dimension(:,:),allocatable :: polthet !(0:3,-ntyp:ntyp)
195 real(kind=8),dimension(:,:),allocatable :: gthet !(3,-ntyp:ntyp)
196 ! Parameters of the side-chain probability distribution
198 real(kind=8),dimension(:),allocatable :: dsc,dsc_inv,dsc0 !(ntyp1)
199 real(kind=8),dimension(:,:),allocatable :: bsc !(maxlob,ntyp)
200 real(kind=8),dimension(:,:,:),allocatable :: censc !(3,maxlob,-ntyp:ntyp)
201 real(kind=8),dimension(:,:,:,:),allocatable :: gaussc !(3,3,maxlob,-ntyp:ntyp)
202 integer,dimension(:),allocatable :: nlob !(ntyp1)
203 ! Virtual-bond lenghts
205 real(kind=8) :: vbl,vblinv,vblinv2,vbl_cis,vbl0
207 integer :: loc_start,loc_end,ithet_start,ithet_end,iphi_start,&
208 iphi_end,iphid_start,iphid_end,ibond_start,ibond_end,&
209 ibondp_start,ibondp_end,ivec_start,ivec_end,iset_start,iset_end,&
210 iturn3_start,iturn3_end,iturn4_start,iturn4_end,iint_start,&
211 iint_end,iphi1_start,iphi1_end,itau_start,itau_end,&
212 ilip_start,ilip_end,itube_start,itube_end
213 integer :: ibond_nucl_start,ibond_nucl_end,iphi_nucl_start,&
214 iphi_nucl_end,iphid_nucl_start,iphid_nucl_end,&
215 ibondp_nucl_start,ibondp_nucl_end,ithet_nucl_start,ithet_nucl_end,&
216 loc_start_nucl,loc_end_nucl
217 integer,dimension(:),allocatable :: ibond_displ,ibond_count,&
218 ithet_displ,ithet_count,iphi_displ,iphi_count,iphi1_displ,&
219 iphi1_count,ivec_displ,ivec_count,iset_displ,iset_count,&
220 iint_count,iint_displ !(0:max_fg_procs-1)
221 !-----------------------------------------------------------------------------
224 real(kind=8),dimension(:,:),allocatable :: gcart,gxcart !(3,0:MAXRES)
225 real(kind=8),dimension(:,:),allocatable :: gradcag,gradxag !(3,MAXRES) !!! nie używane
226 ! common /back_constr/
227 integer :: nfrag_back
228 real(kind=8) :: uconst_back
229 real(kind=8),dimension(:),allocatable :: utheta,ugamma,uscdiff !(maxfrag_back)
230 real(kind=8),dimension(:,:,:),allocatable :: wfrag_back !(3,maxfrag_back,maxprocs/20)
231 integer,dimension(:,:,:),allocatable :: ifrag_back !(3,maxfrag_back,maxprocs/20)
232 ! common /qmeas/ in module geometry
233 !-----------------------------------------------------------------------------
236 real(kind=8) :: ss_depth,ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss
237 integer :: ns,nss,nfree
238 integer,dimension(:),allocatable :: iss !(maxss)
240 real(kind=8),dimension(:),allocatable :: dhpb,forcon,dhpb1,fordepth !(maxdim) !el dhpb1 !!! nie używane
242 integer,dimension(:),allocatable :: ihpb,jhpb,ibecarb !(maxdim) !el ibecarb !!! nie używane
243 ! common /restraints/
244 real(kind=8) :: weidis
245 ! common /links_split/
246 integer :: link_start,link_end
247 ! common /dyn_ssbond/
248 real(kind=8) :: Ht,atriss,btriss,ctriss,dtriss
249 integer,dimension(:),allocatable :: idssb,jdssb !(maxdim)
251 logical,dimension(:),allocatable :: dyn_ss_mask !(maxres)
252 !-----------------------------------------------------------------------------
254 ! Parameters of the SCCOR term
256 real(kind=8),dimension(:,:,:,:),allocatable :: v1sccor,v2sccor !(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp)
257 real(kind=8),dimension(:,:,:),allocatable :: v0sccor !(maxterm_sccor,-ntyp:ntyp,-ntyp:ntyp)
259 integer,dimension(:),allocatable :: isccortyp !(-ntyp:ntyp)
260 integer,dimension(:,:),allocatable :: nterm_sccor,nlor_sccor !(-ntyp:ntyp,-ntyp:ntyp)
261 real(kind=8),dimension(:,:,:),allocatable :: vlor1sccor,&
262 vlor2sccor,vlor3sccor !(maxterm_sccor,20,20)
263 real(kind=8),dimension(:,:,:),allocatable :: gloc_sc !(3,0:maxres2,10)
264 real(kind=8),dimension(:,:,:,:),allocatable :: dtauangle !(3,3,3,maxres2)
265 !-----------------------------------------------------------------------------
267 ! Parameters of the SC rotamers (local) term
269 real(kind=8),dimension(:,:),allocatable :: sc_parmin !(maxsccoef,ntyp)
270 real(kind=8),dimension(:,:),allocatable :: sc_parmin_nucl !(maxsccoef,ntyp)
272 !-----------------------------------------------------------------------------
275 integer :: ndih_constr,ndih_nconstr,ntheta_constr
276 integer,dimension(:),allocatable :: idih_constr,idih_nconstr,itheta_constr !(maxdih_constr)
277 integer :: idihconstr_start,idihconstr_end, &
278 ithetaconstr_start,ithetaconstr_end
279 ! real(kind=8) :: ftors
280 real(kind=8),dimension(:),allocatable :: drange,theta_constr0,theta_drange !(maxdih_constr)
281 real(kind=8),dimension(:),allocatable :: phi0,ftors !(maxdih_constr)
282 real(kind=8),dimension(:),allocatable :: for_thet_constr !(maxdih_constr)
284 !-----------------------------------------------------------------------------
286 ! Torsional constants of the rotation about virtual-bond dihedral angles
288 real(kind=8),dimension(:,:,:),allocatable :: v0 !(-maxtor:maxtor,-maxtor:maxtor,2)
290 real(kind=8),dimension(:,:,:),allocatable :: v1,v2 !(maxterm,-maxtor:maxtor,-maxtor:maxtor)
292 real(kind=8),dimension(:,:,:,:),allocatable :: v1,v2 !(maxterm,-maxtor:maxtor,-maxtor:maxtor,2)
294 real(kind=8),dimension(:,:,:),allocatable :: vlor1 !(maxlor,-maxtor:maxtor,-maxtor:maxtor)
295 real(kind=8),dimension(:,:,:),allocatable :: vlor2,vlor3 !(maxlor,maxtor,maxtor)
296 integer,dimension(:),allocatable :: itortyp !(-ntyp1:ntyp1)
297 integer,dimension(:,:,:),allocatable :: nterm,nlor !(-maxtor:maxtor,-maxtor:maxtor,2)
298 integer :: ntortyp,nterm_old
299 !------torsion nucleic
300 real(kind=8),dimension(:,:),allocatable :: v0_nucl !(-maxtor:maxtor,-maxtor:maxtor,2)
301 real(kind=8),dimension(:,:,:),allocatable :: v1_nucl,v2_nucl !(maxterm,-maxtor:maxtor,-maxtor:maxtor)
302 real(kind=8),dimension(:,:,:),allocatable :: vlor1_nucl !(maxlor,-maxtor:maxtor,-maxtor:maxtor)
303 real(kind=8),dimension(:,:,:),allocatable :: vlor2_nucl,vlor3_nucl !(maxlor,maxtor,maxtor)
304 integer,dimension(:),allocatable :: itortyp_nucl !(-ntyp1:ntyp1)
305 integer,dimension(:,:),allocatable :: nterm_nucl,nlor_nucl !(-maxtor:maxtor,-maxtor:maxtor,2)
306 integer :: ntortyp_nucl,nterm_old_nucl
308 ! 6/23/01 - constants for double torsionals
310 real(kind=8),dimension(:,:,:,:,:,:),allocatable :: v1c,v1s
311 !(2,maxtermd_1,-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2)
312 real(kind=8),dimension(:,:,:,:,:,:),allocatable :: v2c,v2s
313 !(maxtermd_2,maxtermd_2,-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2)
314 integer,dimension(:,:,:,:),allocatable :: ntermd_1,ntermd_2
315 !(-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2)
316 ! 9/18/99 - added Fourier coeffficients of the expansion of local energy
319 real(kind=8),dimension(:,:),allocatable :: b1,b2,&
320 b1tilde !(2,-maxtor:maxtor),
321 real(kind=8),dimension(:,:,:),allocatable :: cc,dd,ee,&
322 ctilde,dtilde !(2,2,-maxtor:maxtor)
324 ! common/fourier/ z wham
325 real(kind=8),dimension(:,:),allocatable :: b !(13,0:maxtor)
326 !---------------MOMO---------------------------------------------------
327 integer,dimension(:),allocatable :: icharge
328 real(kind=8),dimension(:,:),allocatable :: alphapol,epshead,&
329 sig0head,sigiso1,sigiso2,rborn,sigmap1,sigmap2,chis,wquad,chipp,&
331 real(kind=8),dimension(:,:,:),allocatable :: alphasur,alphiso,&
333 real(kind=8),dimension(:,:,:,:),allocatable :: dhead
334 !-----------------------------------------------------------------------------
336 ! Varibles for cutoff on electorstatic
337 real(kind=8) sss_ele_cut,sss_ele_grad
338 integer xshift,yshift,zshift
339 !2 Jul 2017 lipidc parameters -----------------------------------------------------
340 real(kind=8),dimension(:), allocatable :: liptranene
341 real(kind=8) :: pepliptran
343 ! 4 Jul 2017 parameters for shieliding
344 real(kind=8),dimension(:), allocatable :: long_r_sidechain, &
346 real(kind=8) :: VSolvSphere,VSolvSphere_div,buff_shield
348 real(kind=8) :: distafminit,forceAFMconst,velAFMconst
349 integer :: afmend,afmbeg
350 real(kind=8),dimension(:,:), allocatable :: catprm
352 real(kind=8),dimension(:,:), allocatable :: eps_scbase, &
354 sigmap1_scbase,sigmap2_scbase, &
355 dhead_scbasei, dhead_scbasej, epshead_scbase,&
356 sig0head_scbase, rborn_scbasei,rborn_scbasej,alphapol_scbase,epsintab_scbase,&
358 real(kind=8),dimension(:,:,:), allocatable :: alphasur_scbase, &
359 wdipdip_scbase,wqdip_scbase,chi_scbase,chipp_scbase,chis_scbase
361 real(kind=8),dimension(:), allocatable :: eps_pepbase, &
363 sigmap1_pepbase,sigmap2_pepbase,&
364 aa_pepbase,bb_pepbase
366 real(kind=8),dimension(:,:), allocatable :: alphasur_pepbase, &
367 wdipdip_pepbase,chi_pepbase,chipp_pepbase,chis_pepbase
369 real(kind=8),dimension(:), allocatable :: eps_scpho, &
371 sigmap1_scpho,sigmap2_scpho,&
372 aa_scpho,bb_scpho,wqq_scpho,epsintab_scpho,alphapol_scpho,&
373 rborn_scphoi,rborn_scphoj,dhead_scphoi,alphi_scpho
375 real(kind=8),dimension(:,:), allocatable :: alphasur_scpho, &
376 chi_scpho,chipp_scpho,chis_scpho, &
378 real(kind=8) ,dimension(4) :: alphasur_peppho
379 real(kind=8) ,dimension(2) :: wqdip_peppho
380 real(kind=8) :: eps_peppho,sigma_peppho,sigmap1_peppho,sigmap2_peppho, &
382 end module energy_data